The Manhattan plot is a common way to visualize p-values or log-odds ratios for GWAS studies across genomic coordinates.
The starting point for a Manhattan plot is a spreadsheet with SNPs on rows and p-values or log-odds ratios in a column. If beginning with p-values, you will need to convert the p-values to -log10(p-value).
- Select the column with p-values
- Select Transform form the main toolbar
- Select Normalization & Scaling
- Select On Columns...
- In the Normalization tab, set Base of the Log(x + offset) to 10
- Select OK
- Go to Transform > Normalization & Scaling > On Columns... again
- Select the Add/Mul/Sub/Div tab
- Set Multiply by Constant to -1
- Select OK
The column now contains -log10(p-value).
We can now invoke the initial plot.
- Select View from the main toolbar
- Select Genome View
The Genome View tab will open. This plot will need to be configured.
- Select ( ) from the plot command bar
- Select the Profiles tab
- Remove any unwanted profiles
- Select Add profile
- Select Column
- Select the column with the -log10(p-value) or logs-odds ratio values from the drop-down menu
- Select Value for Color by
- Select point from the Style drop-down menu
- Select OK to add the profile
- Select OK to close the Configure Plot Properties dialog
The plot will now show a Manhattan plot.
For details on Genome View see Chapter 6: The Pattern Visualization System in the Partek User's Manual.
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